| plot_rmd_snakemake |
1 |
- docs/html/plot_rmd_snakemake.html
|
|
|
|
| plot_rmd_shell |
1 |
- docs/html/plot_rmd_shell.html
- docs/png/plot_rmd_shell.png
|
|
|
| R -e 'wd = getwd(); rmarkdown::render( "{input[0]}", output_file = normalizePath( paste0( wd,"/" ,"{output[0]}" ) ), params = list(input = "{input[1]}", output = "{output[1]}" ), knit_root_dir = getwd(), envir = new.env() )'
|
|
| plot_nb_2_html |
1 |
- docs/html/plot_jup_nb.html
|
|
- _libgcc_mutex=0.1=main
- ansiwrap=0.8.4=py_0
- arrow-cpp=0.13.0=py36h117bdfb_0
- asn1crypto=1.2.0=py36_0
- attrs=19.3.0=py_0
- backcall=0.1.0=py36_0
- backports=1.0=py_2
- backports.tempfile=1.0=py_1
- backports.weakref=1.0.post1=py_1
- blas=1.0=mkl
- bleach=3.1.0=py36_0
- boost-cpp=1.67.0=h14c3975_4
- brotli=1.0.7=he6710b0_0
- bzip2=1.0.8=h7b6447c_0
- ca-certificates=2019.11.28=hecc5488_0
- certifi=2019.11.28=py36_0
- cffi=1.13.2=py36h2e261b9_0
- chardet=3.0.4=py36_1003
- click=7.0=py36_0
- cryptography=2.8=py36h1ba5d50_0
- cycler=0.10.0=py36_0
- dbus=1.13.12=h746ee38_0
- decorator=4.4.1=py_0
- defusedxml=0.6.0=py_0
- double-conversion=3.1.5=he6710b0_1
- entrypoints=0.3=py36_0
- expat=2.2.6=he6710b0_0
- feather-format=0.4.0=py_1003
- fontconfig=2.13.0=h9420a91_0
- freetype=2.9.1=h8a8886c_1
- future=0.18.2=py36_0
- gflags=2.2.2=he6710b0_0
- glib=2.63.1=h5a9c865_0
- glog=0.4.0=he6710b0_0
- gmp=6.1.2=h6c8ec71_1
- gst-plugins-base=1.14.0=hbbd80ab_1
- gstreamer=1.14.0=hb453b48_1
- icu=58.2=h9c2bf20_1
- idna=2.8=py36_0
- importlib_metadata=1.3.0=py36_0
- intel-openmp=2019.4=243
- ipykernel=5.1.3=py36h39e3cac_0
- ipython=7.10.2=py36h39e3cac_0
- ipython_genutils=0.2.0=py36_0
- ipywidgets=7.5.1=py_0
- jedi=0.15.1=py36_0
- jinja2=2.10.3=py_0
- jpeg=9b=h024ee3a_2
- jsonschema=3.2.0=py36_0
- jupyter=1.0.0=py36_7
- jupyter_client=5.3.4=py36_0
- jupyter_console=6.0.0=py36_0
- jupyter_core=4.6.1=py36_0
- kiwisolver=1.1.0=py36he6710b0_0
- libboost=1.67.0=h46d08c1_4
- libedit=3.1.20181209=hc058e9b_0
- libevent=2.1.8=h1ba5d50_0
- libffi=3.2.1=hd88cf55_4
- libgcc-ng=9.1.0=hdf63c60_0
- libgfortran-ng=7.3.0=hdf63c60_0
- libpng=1.6.37=hbc83047_0
- libprotobuf=3.6.0=hdbcaa40_0
- libsodium=1.0.16=h1bed415_0
- libstdcxx-ng=9.1.0=hdf63c60_0
- libuuid=1.0.3=h1bed415_2
- libxcb=1.13=h1bed415_1
- libxml2=2.9.9=hea5a465_1
- lz4-c=1.8.1.2=h14c3975_0
- markupsafe=1.1.1=py36h7b6447c_0
- matplotlib=3.1.1=py36h5429711_0
- mistune=0.8.4=py36h7b6447c_0
- mkl=2019.4=243
- mkl-service=2.3.0=py36he904b0f_0
- mkl_fft=1.0.15=py36ha843d7b_0
- mkl_random=1.1.0=py36hd6b4f25_0
- more-itertools=7.2.0=py36_0
- nb_conda=2.2.1=py36_0
- nb_conda_kernels=2.2.2=py36_0
- nbconvert=5.6.1=py36_0
- nbformat=4.4.0=py36_0
- ncurses=6.1=he6710b0_1
- notebook=6.0.2=py36_0
- numpy=1.17.4=py36hc1035e2_0
- numpy-base=1.17.4=py36hde5b4d6_0
- openssl=1.1.1d=h516909a_0
- pandas=0.25.3=py36he6710b0_0
- pandoc=2.2.3.2=0
- pandocfilters=1.4.2=py36_1
- papermill=1.2.1=py36_0
- parso=0.5.2=py_0
- patsy=0.5.1=py36_0
- pcre=8.43=he6710b0_0
- pexpect=4.7.0=py36_0
- pickleshare=0.7.5=py36_0
- pip=19.3.1=py36_0
- plotly=4.3.0=py_0
- plotly_express=0.4.1=py_0
- prometheus_client=0.7.1=py_0
- prompt_toolkit=2.0.9=py36_0
- ptyprocess=0.6.0=py36_0
- pyaml=19.4.1=py_0
- pyarrow=0.13.0=py36he6710b0_0
- pycparser=2.19=py36_0
- pygments=2.5.2=py_0
- pyopenssl=19.1.0=py36_0
- pyparsing=2.4.5=py_0
- pyqt=5.9.2=py36h05f1152_2
- pyrsistent=0.15.6=py36h7b6447c_0
- pysocks=1.7.1=py36_0
- python=3.6.9=h265db76_0
- python-dateutil=2.8.1=py_0
- pytz=2019.3=py_0
- pyyaml=5.2=py36h7b6447c_0
- pyzmq=18.1.0=py36he6710b0_0
- qt=5.9.7=h5867ecd_1
- qtconsole=4.6.0=py_0
- re2=2019.08.01=he6710b0_0
- readline=7.0=h7b6447c_5
- requests=2.22.0=py36_1
- retrying=1.3.3=py36_2
- scipy=1.3.2=py36h7c811a0_0
- seaborn=0.9.0=pyh91ea838_1
- send2trash=1.5.0=py36_0
- setuptools=42.0.2=py36_0
- sip=4.19.8=py36hf484d3e_0
- six=1.13.0=py36_0
- snappy=1.1.7=hbae5bb6_3
- sqlite=3.30.1=h7b6447c_0
- statsmodels=0.10.1=py36hdd07704_0
- tenacity=6.0.0=py36_0
- terminado=0.8.3=py36_0
- testpath=0.4.4=py_0
- textwrap3=0.9.2=py_0
- thrift-cpp=0.11.0=h02b749d_3
- tk=8.6.8=hbc83047_0
- tornado=6.0.3=py36h7b6447c_0
- tqdm=4.40.2=py_0
- traitlets=4.3.3=py36_0
- urllib3=1.25.7=py36_0
- wcwidth=0.1.7=py36_0
- webencodings=0.5.1=py36_1
- wheel=0.33.6=py36_0
- widgetsnbextension=3.5.1=py36_0
- xz=5.2.4=h14c3975_4
- yaml=0.1.7=had09818_2
- zeromq=4.3.1=he6710b0_3
- zipp=0.6.0=py_0
- zlib=1.2.11=h7b6447c_3
- zstd=1.3.7=h0b5b093_0
- {'pip': ['appdirs==1.4.3', 'configargparse==0.15.2', 'datrie==0.8', 'docutils==0.15.2', 'gitdb2==2.0.6', 'gitpython==3.0.5', 'psutil==5.6.7', 'ratelimiter==1.2.0.post0', 'smmap2==2.0.5', 'snakemake==5.8.2', 'wrapt==1.11.2']}
|
| jupyter nbconvert --to html {input} --output ../../../{output}
|
|
| load_dataset |
1 |
- data/out/feather/data.feather
|
|
- _libgcc_mutex=0.1=main
- ansiwrap=0.8.4=py_0
- arrow-cpp=0.13.0=py36h117bdfb_0
- asn1crypto=1.2.0=py36_0
- attrs=19.3.0=py_0
- backcall=0.1.0=py36_0
- backports=1.0=py_2
- backports.tempfile=1.0=py_1
- backports.weakref=1.0.post1=py_1
- blas=1.0=mkl
- bleach=3.1.0=py36_0
- boost-cpp=1.67.0=h14c3975_4
- brotli=1.0.7=he6710b0_0
- bzip2=1.0.8=h7b6447c_0
- ca-certificates=2019.11.28=hecc5488_0
- certifi=2019.11.28=py36_0
- cffi=1.13.2=py36h2e261b9_0
- chardet=3.0.4=py36_1003
- click=7.0=py36_0
- cryptography=2.8=py36h1ba5d50_0
- cycler=0.10.0=py36_0
- dbus=1.13.12=h746ee38_0
- decorator=4.4.1=py_0
- defusedxml=0.6.0=py_0
- double-conversion=3.1.5=he6710b0_1
- entrypoints=0.3=py36_0
- expat=2.2.6=he6710b0_0
- feather-format=0.4.0=py_1003
- fontconfig=2.13.0=h9420a91_0
- freetype=2.9.1=h8a8886c_1
- future=0.18.2=py36_0
- gflags=2.2.2=he6710b0_0
- glib=2.63.1=h5a9c865_0
- glog=0.4.0=he6710b0_0
- gmp=6.1.2=h6c8ec71_1
- gst-plugins-base=1.14.0=hbbd80ab_1
- gstreamer=1.14.0=hb453b48_1
- icu=58.2=h9c2bf20_1
- idna=2.8=py36_0
- importlib_metadata=1.3.0=py36_0
- intel-openmp=2019.4=243
- ipykernel=5.1.3=py36h39e3cac_0
- ipython=7.10.2=py36h39e3cac_0
- ipython_genutils=0.2.0=py36_0
- ipywidgets=7.5.1=py_0
- jedi=0.15.1=py36_0
- jinja2=2.10.3=py_0
- jpeg=9b=h024ee3a_2
- jsonschema=3.2.0=py36_0
- jupyter=1.0.0=py36_7
- jupyter_client=5.3.4=py36_0
- jupyter_console=6.0.0=py36_0
- jupyter_core=4.6.1=py36_0
- kiwisolver=1.1.0=py36he6710b0_0
- libboost=1.67.0=h46d08c1_4
- libedit=3.1.20181209=hc058e9b_0
- libevent=2.1.8=h1ba5d50_0
- libffi=3.2.1=hd88cf55_4
- libgcc-ng=9.1.0=hdf63c60_0
- libgfortran-ng=7.3.0=hdf63c60_0
- libpng=1.6.37=hbc83047_0
- libprotobuf=3.6.0=hdbcaa40_0
- libsodium=1.0.16=h1bed415_0
- libstdcxx-ng=9.1.0=hdf63c60_0
- libuuid=1.0.3=h1bed415_2
- libxcb=1.13=h1bed415_1
- libxml2=2.9.9=hea5a465_1
- lz4-c=1.8.1.2=h14c3975_0
- markupsafe=1.1.1=py36h7b6447c_0
- matplotlib=3.1.1=py36h5429711_0
- mistune=0.8.4=py36h7b6447c_0
- mkl=2019.4=243
- mkl-service=2.3.0=py36he904b0f_0
- mkl_fft=1.0.15=py36ha843d7b_0
- mkl_random=1.1.0=py36hd6b4f25_0
- more-itertools=7.2.0=py36_0
- nb_conda=2.2.1=py36_0
- nb_conda_kernels=2.2.2=py36_0
- nbconvert=5.6.1=py36_0
- nbformat=4.4.0=py36_0
- ncurses=6.1=he6710b0_1
- notebook=6.0.2=py36_0
- numpy=1.17.4=py36hc1035e2_0
- numpy-base=1.17.4=py36hde5b4d6_0
- openssl=1.1.1d=h516909a_0
- pandas=0.25.3=py36he6710b0_0
- pandoc=2.2.3.2=0
- pandocfilters=1.4.2=py36_1
- papermill=1.2.1=py36_0
- parso=0.5.2=py_0
- patsy=0.5.1=py36_0
- pcre=8.43=he6710b0_0
- pexpect=4.7.0=py36_0
- pickleshare=0.7.5=py36_0
- pip=19.3.1=py36_0
- plotly=4.3.0=py_0
- plotly_express=0.4.1=py_0
- prometheus_client=0.7.1=py_0
- prompt_toolkit=2.0.9=py36_0
- ptyprocess=0.6.0=py36_0
- pyaml=19.4.1=py_0
- pyarrow=0.13.0=py36he6710b0_0
- pycparser=2.19=py36_0
- pygments=2.5.2=py_0
- pyopenssl=19.1.0=py36_0
- pyparsing=2.4.5=py_0
- pyqt=5.9.2=py36h05f1152_2
- pyrsistent=0.15.6=py36h7b6447c_0
- pysocks=1.7.1=py36_0
- python=3.6.9=h265db76_0
- python-dateutil=2.8.1=py_0
- pytz=2019.3=py_0
- pyyaml=5.2=py36h7b6447c_0
- pyzmq=18.1.0=py36he6710b0_0
- qt=5.9.7=h5867ecd_1
- qtconsole=4.6.0=py_0
- re2=2019.08.01=he6710b0_0
- readline=7.0=h7b6447c_5
- requests=2.22.0=py36_1
- retrying=1.3.3=py36_2
- scipy=1.3.2=py36h7c811a0_0
- seaborn=0.9.0=pyh91ea838_1
- send2trash=1.5.0=py36_0
- setuptools=42.0.2=py36_0
- sip=4.19.8=py36hf484d3e_0
- six=1.13.0=py36_0
- snappy=1.1.7=hbae5bb6_3
- sqlite=3.30.1=h7b6447c_0
- statsmodels=0.10.1=py36hdd07704_0
- tenacity=6.0.0=py36_0
- terminado=0.8.3=py36_0
- testpath=0.4.4=py_0
- textwrap3=0.9.2=py_0
- thrift-cpp=0.11.0=h02b749d_3
- tk=8.6.8=hbc83047_0
- tornado=6.0.3=py36h7b6447c_0
- tqdm=4.40.2=py_0
- traitlets=4.3.3=py36_0
- urllib3=1.25.7=py36_0
- wcwidth=0.1.7=py36_0
- webencodings=0.5.1=py36_1
- wheel=0.33.6=py36_0
- widgetsnbextension=3.5.1=py36_0
- xz=5.2.4=h14c3975_4
- yaml=0.1.7=had09818_2
- zeromq=4.3.1=he6710b0_3
- zipp=0.6.0=py_0
- zlib=1.2.11=h7b6447c_3
- zstd=1.3.7=h0b5b093_0
- {'pip': ['appdirs==1.4.3', 'configargparse==0.15.2', 'datrie==0.8', 'docutils==0.15.2', 'gitdb2==2.0.6', 'gitpython==3.0.5', 'psutil==5.6.7', 'ratelimiter==1.2.0.post0', 'smmap2==2.0.5', 'snakemake==5.8.2', 'wrapt==1.11.2']}
|
| import seaborn as sns
import pandas as pd
params = snakemake.config
df = sns.load_dataset(params['dataset'])
df.to_feather(snakemake.output[0])
print('load finished')
|
|
| plot_execute_nb_plot |
1 |
- src/nb/executed/plot.ipynb
|
|
- _libgcc_mutex=0.1=main
- ansiwrap=0.8.4=py_0
- arrow-cpp=0.13.0=py36h117bdfb_0
- asn1crypto=1.2.0=py36_0
- attrs=19.3.0=py_0
- backcall=0.1.0=py36_0
- backports=1.0=py_2
- backports.tempfile=1.0=py_1
- backports.weakref=1.0.post1=py_1
- blas=1.0=mkl
- bleach=3.1.0=py36_0
- boost-cpp=1.67.0=h14c3975_4
- brotli=1.0.7=he6710b0_0
- bzip2=1.0.8=h7b6447c_0
- ca-certificates=2019.11.28=hecc5488_0
- certifi=2019.11.28=py36_0
- cffi=1.13.2=py36h2e261b9_0
- chardet=3.0.4=py36_1003
- click=7.0=py36_0
- cryptography=2.8=py36h1ba5d50_0
- cycler=0.10.0=py36_0
- dbus=1.13.12=h746ee38_0
- decorator=4.4.1=py_0
- defusedxml=0.6.0=py_0
- double-conversion=3.1.5=he6710b0_1
- entrypoints=0.3=py36_0
- expat=2.2.6=he6710b0_0
- feather-format=0.4.0=py_1003
- fontconfig=2.13.0=h9420a91_0
- freetype=2.9.1=h8a8886c_1
- future=0.18.2=py36_0
- gflags=2.2.2=he6710b0_0
- glib=2.63.1=h5a9c865_0
- glog=0.4.0=he6710b0_0
- gmp=6.1.2=h6c8ec71_1
- gst-plugins-base=1.14.0=hbbd80ab_1
- gstreamer=1.14.0=hb453b48_1
- icu=58.2=h9c2bf20_1
- idna=2.8=py36_0
- importlib_metadata=1.3.0=py36_0
- intel-openmp=2019.4=243
- ipykernel=5.1.3=py36h39e3cac_0
- ipython=7.10.2=py36h39e3cac_0
- ipython_genutils=0.2.0=py36_0
- ipywidgets=7.5.1=py_0
- jedi=0.15.1=py36_0
- jinja2=2.10.3=py_0
- jpeg=9b=h024ee3a_2
- jsonschema=3.2.0=py36_0
- jupyter=1.0.0=py36_7
- jupyter_client=5.3.4=py36_0
- jupyter_console=6.0.0=py36_0
- jupyter_core=4.6.1=py36_0
- kiwisolver=1.1.0=py36he6710b0_0
- libboost=1.67.0=h46d08c1_4
- libedit=3.1.20181209=hc058e9b_0
- libevent=2.1.8=h1ba5d50_0
- libffi=3.2.1=hd88cf55_4
- libgcc-ng=9.1.0=hdf63c60_0
- libgfortran-ng=7.3.0=hdf63c60_0
- libpng=1.6.37=hbc83047_0
- libprotobuf=3.6.0=hdbcaa40_0
- libsodium=1.0.16=h1bed415_0
- libstdcxx-ng=9.1.0=hdf63c60_0
- libuuid=1.0.3=h1bed415_2
- libxcb=1.13=h1bed415_1
- libxml2=2.9.9=hea5a465_1
- lz4-c=1.8.1.2=h14c3975_0
- markupsafe=1.1.1=py36h7b6447c_0
- matplotlib=3.1.1=py36h5429711_0
- mistune=0.8.4=py36h7b6447c_0
- mkl=2019.4=243
- mkl-service=2.3.0=py36he904b0f_0
- mkl_fft=1.0.15=py36ha843d7b_0
- mkl_random=1.1.0=py36hd6b4f25_0
- more-itertools=7.2.0=py36_0
- nb_conda=2.2.1=py36_0
- nb_conda_kernels=2.2.2=py36_0
- nbconvert=5.6.1=py36_0
- nbformat=4.4.0=py36_0
- ncurses=6.1=he6710b0_1
- notebook=6.0.2=py36_0
- numpy=1.17.4=py36hc1035e2_0
- numpy-base=1.17.4=py36hde5b4d6_0
- openssl=1.1.1d=h516909a_0
- pandas=0.25.3=py36he6710b0_0
- pandoc=2.2.3.2=0
- pandocfilters=1.4.2=py36_1
- papermill=1.2.1=py36_0
- parso=0.5.2=py_0
- patsy=0.5.1=py36_0
- pcre=8.43=he6710b0_0
- pexpect=4.7.0=py36_0
- pickleshare=0.7.5=py36_0
- pip=19.3.1=py36_0
- plotly=4.3.0=py_0
- plotly_express=0.4.1=py_0
- prometheus_client=0.7.1=py_0
- prompt_toolkit=2.0.9=py36_0
- ptyprocess=0.6.0=py36_0
- pyaml=19.4.1=py_0
- pyarrow=0.13.0=py36he6710b0_0
- pycparser=2.19=py36_0
- pygments=2.5.2=py_0
- pyopenssl=19.1.0=py36_0
- pyparsing=2.4.5=py_0
- pyqt=5.9.2=py36h05f1152_2
- pyrsistent=0.15.6=py36h7b6447c_0
- pysocks=1.7.1=py36_0
- python=3.6.9=h265db76_0
- python-dateutil=2.8.1=py_0
- pytz=2019.3=py_0
- pyyaml=5.2=py36h7b6447c_0
- pyzmq=18.1.0=py36he6710b0_0
- qt=5.9.7=h5867ecd_1
- qtconsole=4.6.0=py_0
- re2=2019.08.01=he6710b0_0
- readline=7.0=h7b6447c_5
- requests=2.22.0=py36_1
- retrying=1.3.3=py36_2
- scipy=1.3.2=py36h7c811a0_0
- seaborn=0.9.0=pyh91ea838_1
- send2trash=1.5.0=py36_0
- setuptools=42.0.2=py36_0
- sip=4.19.8=py36hf484d3e_0
- six=1.13.0=py36_0
- snappy=1.1.7=hbae5bb6_3
- sqlite=3.30.1=h7b6447c_0
- statsmodels=0.10.1=py36hdd07704_0
- tenacity=6.0.0=py36_0
- terminado=0.8.3=py36_0
- testpath=0.4.4=py_0
- textwrap3=0.9.2=py_0
- thrift-cpp=0.11.0=h02b749d_3
- tk=8.6.8=hbc83047_0
- tornado=6.0.3=py36h7b6447c_0
- tqdm=4.40.2=py_0
- traitlets=4.3.3=py36_0
- urllib3=1.25.7=py36_0
- wcwidth=0.1.7=py36_0
- webencodings=0.5.1=py36_1
- wheel=0.33.6=py36_0
- widgetsnbextension=3.5.1=py36_0
- xz=5.2.4=h14c3975_4
- yaml=0.1.7=had09818_2
- zeromq=4.3.1=he6710b0_3
- zipp=0.6.0=py_0
- zlib=1.2.11=h7b6447c_3
- zstd=1.3.7=h0b5b093_0
- {'pip': ['appdirs==1.4.3', 'configargparse==0.15.2', 'datrie==0.8', 'docutils==0.15.2', 'gitdb2==2.0.6', 'gitpython==3.0.5', 'psutil==5.6.7', 'ratelimiter==1.2.0.post0', 'smmap2==2.0.5', 'snakemake==5.8.2', 'wrapt==1.11.2']}
|
| python -c 'import papermill as pm; pm.execute_notebook( "{input[0]}" , "{output[0]}" , parameters = dict( input = "{input[1]}") )'
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|